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Multivariate genomic models

Model

The genomic models can be extended to a multivariate setup. The textbook focuses on multivariate GBLUP and gives a numerical example for this model. Users can apply the same techniques and tricks discussed in the previous sections to multivariate genomic models.

Please see the textbook for details.

Files

In the textbook, the author compares breeding-value solutions between the pedigree-based and genomic (GBLUP) models. Both models use the same data set (mr1113.dat), which is also used in Table 6.1 (Chapter 6) of the textbook (p. 210).

For the pedigree BLUP model, the pedigree file mr1113a.ped is used. For GBLUP, the pedigree file (mr1113b.ped) is a dummy file. The genotype file (mr1113.gen) and the cross-reference file (mr1113.xrf) are used exclusively for GBLUP.

Each model needs a separate parameter file. In the GitHub repository, the user can find mr1113a.par for the pedigree model and mr1113b.par for GBLUP.

Solutions

The calculated solutions are identical to those in the textbook (p. 211).

Note that, as stated in the textbook, the comparison between the models (pedigree BLUP versus GBLUP) is not valid because the data contain only 10 SNP markers. Too few markers tend to result in an inaccurate \(\mathbf{G}\), which may lead to unstable genomic predictions. Therefore, this numerical example should be viewed as a demonstration of multivariate analysis with GBLUP.

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